What makes some cookies flat and crispy and others soft and chewy has a lot to do with the amount and temperature of key ingrdients:

Sugar:  The moisture in sugar affects chewiness. The relative amount of white granulated sugar to brown sugar has a great effect on the baked cookie, as the brown sugar has a much higher moisture content (approximately 35% more moisture). Also, brown sugar contains invert sugar, which is all but absent in white granulated sugar. Invert sugar consists of glucose and fructose, two simple sugars. Invert sugar is especially hydroscopic, meaning that it absorbs water from wherever it can be found, the best source being the air. And invert sugar continues to absorb moisture even after the cookies have been baked, thus keeping them chewy as they cool. therefore, using more brown sugar will result in softer, chewier cookies, while using more white granulated sugar will result in cookies that are flatter and crisper overall.

Butter and Eggs:  The temperature of these key ingredients helps to control how much the dough spreads. Cool ingredients will keep your dough cooler, which results in the cookies spreading more slowly in the oven allowing the oven's heat to "set" the cookie while it is still thick and therefore producing a denser, chewier cookie. Warm dough spreads more quickly in the oven, which makes the cookies thinner and crisper. Also, keep this theory in mind if you have the habit of dropping cookies onto still-hot cookie sheets. If you don't want them spreading quickly, use cool sheets.

Flour:  A high proportion of butter to flour in the dough will also allow it to spread quickly. make sure you are your flour correctly. Adding more flour to a recipe to produce a thick chewy cookie won't work. Too much flour will make the cookie firm, dry and tough you need to control the amount and temperature of all key ingredents together and that includes the butter, eggs, sugar and flour. To insure that you are accurately using the amount of flour called for in the recipe, use a kitchen scale to weigh it or measure properly: use a dry measuring cup, not a pyrex cup meant to liquid measurements. Fluff the flour with a fork to avoid densely packed flour. then spoon the flour into the measuring cup and level it with a knife. Never scoop right from the bag or container as that will compact too much flour into the cup, and don't shale or tap the cup as you add the flour or this will pack the flour down as well.

One last tip:  Bake cookies on light colored cookie sheets derk cookie sheets will cause the cookies to brown too quickly and cook too fast. If all you have is dark cookie sheets, try baking your cookies on parchment paper lined cookie sheets. You'll be surprised at the difference it makes. Cookies also cook more evenly on cookie sheets that do not have side as the heat flows over the cookies more eveny.

[edited June-20-2008]